Population Epigenetics and Epigenomics

Our DNA stores heritable information in the form of a four letter code; A, C, G and T. Textbook genetics tells us that the code can be mutated (e.g. letter A turns into letter G), and that such mutations alter the functions of genes. In plants, it is becoming increasingly clear that heritable alterations in gene function can also be caused by meiotically stable epimutations, which arise independently of DNA changes. A well-known example of an epimutation is the accidental gain or loss of DNA methylation, the chemical modification of a cytosine (the letter C in the DNA code) into 5-methylcytosine.   

We have previously shown that experimentally-induced as well as spontaneously occurring epimutations can be remarkably stable across generations, and can in some cases even contribute to the heritability of important plant traits. Because of these observations, epigenetic modifications - such as DNA methylation - have emerged as potentially important factors in plant evolution, and as possible molecular targets for the improvement of commercial crops.   

The focus group Population epigenetics and epigenomics aims to explore the agricultural and evolutionary implications of heritable epimutations in plants. One major aspect of this work is the development of computational methods for the analysis of population-level epigenomic sequencing data. The goal is to find efficient ways to detect ‘epimutatable’ regions in plant genomes, and to characterize these regions in terms of epigenomic patterns of variation both within and across plant species. A second aspect of our work is to infer the sources, stability and phenotypic impact of heritable epimutations either by direct observation of multi-generational data, or indirectly by using inference methods from evolutionary genetics.  

The focus group consists of TUM-IAS Rudolf Mößbauer Tenure Track Prof. Frank Johannes (TUM School of Life Sciences Weihenstephan), TUM-IAS Hans Fischer Fellow Prof. Robert J. Schmitz (University of Georgia), postdoctoral researcher Dr. Rashmi Hazarika (TUM School of Life Sciences Weihenstephan) and TUM-IAS funded doctoral candidate Talha Mubeen (TUM School of Life Sciences Weihenstephan).

Publications by the Focus Group

2018

  • Johannes, Frank; Schmitz, Robert J.: Spontaneous epimutations in plants. New Phytologist 221 (3), 2018, 1253-1259 mehr…

2017

  • Lauss, Kathrin; Wardenaar, René; Oka, Rurika; van Hulten, Marieke H. A.; Guryev, Victor; Keurentjes, Joost J. B.; Stam, Maike; Johannes, Frank: Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids. Plant Physiology 176 (2), 2017, 1627-1645 mehr…
  • Morgado, Lionel; Johannes, Frank: Computational tools for plant small RNA detection and categorization. Briefings in Bioinformatics, 2017 mehr…
  • Morgado, Lionel; Preite, Veronica; Oplaat, Carla; Anava, Sarit; Ferreira de Carvalho, Julie; Rechavi, Oded; Johannes, Frank; Verhoeven, Koen J.F.: Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Molecular Biology and Evolution 34 (8), 2017, 2035-2040 mehr…

2016

  • Diao, Wenwen; Mousset, Mathilde; Horsburgh, Gavin J.; Vermeulen, Cornelis J.; Johannes, Frank; van de Zande, Louis; Ritchie, Michael G.; Schmitt, Thomas; Beukeboom, Leo W.: Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps. G3: Genes|Genomes|Genetics 6 (6), 2016, 1549-1562 mehr…
  • Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank: Genetic sources of population epigenomic variation. Nature Reviews Genetics 17 (6), 2016, 319-332 mehr…
  • Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank: Methylome evolution in plants. Genome Biology 17 (1), 2016 mehr…